[BioC] segfault in rqubic

[Eric Liaw [guest]]

Hello,

I ran into a segfault while trying to run rqubic on a 2189x9779 matrix of integers (actually of mode 'numeric', named "data.exp.discr...") with values 0 through 6 (not a microarray dataset). I'm not sure if the error is in the way I made the rqubicSeeds and ExpressionSet objects from my matrix, or something internal to rqubic. The segfault is reproducible and occurs a few seconds after calling the function.

The error message is copied below.

Thanks,
Eric Liaw
undergraduate student, Stanford University
-------------------------------------

> data.exprs <- new("ExpressionSet", data) #data is a matrix.
> data.seeds <- generateSeeds(object=data.exprs)

Warning message:
In .local(object, ...) :
  'generateSeeds' requires an matrix of integer. Coerced

> QUBIC.1 <- quBicluster(seeds=data.seeds, eset=data.exprs, report.no=30)

 *** caught segfault ***
address 0xffffffff1efabdd0, cause 'memory not mapped'

Traceback:
 1: .Call("qubicluster", seeds = seeds, exprs = exp.leveled, sigma_val = sigma,     symbols = symbols, report_no = report.no, tolerance_val = tolerance,     filter_proportion = filter.proportion)
 2: quBiclusterIndex(seeds = seeds, eset = eset, report.no = report.no,     tolerance = tolerance, filter.proportion = filter.proportion)
 3: quBicluster(seeds = data.seeds,     eset = data.exprs, report.no = 30)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

In quBiclusterIndex(seeds = seeds, eset = eset, report.no = report.no,  :
  'eset' requires an matrix of integer as the value of 'exprs'. Coerced

 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] rqubic_1.4.0       biclust_1.0.2      lattice_0.20-13    colorspace_1.0-1
[5] MASS_7.3-23        Biobase_2.18.0     BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] tools_2.15.2


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